Traditional microbiological work up is slow and sometimes inaccurate, relying on phenotypic culture identification followed by antimicrobial susceptibility testing. Newer technologies, such as matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and real-time molecular detection (antimicrobial resistance genes microarrays) have advanced the diagnostic capabilities of clinical microbiology laboratories and have created an exciting field for research and development. Given the in-depth and highly accurate (sometimes complex) results that are produced by such platforms, careful detailed analyses are required to better understand the clinical significance of the organisms identified and the resistance mechanisms detected. During this fiscal year, we performed a large comparative evaluation of the compendial USP<71> method against the automated Bactec FX system and BacTAlert Dual-T system using 118 organisms recovered from cGMP environments to assess analytical performance for the detection of environmental contaminants in cell therapy products. This study is the largest of its kind to date, and provides strong data to support the clinical application of certain automated culture systems and settings, if supplemented with improved fungal detection methods, as an alternative method to the USP<71> compendial method. The limitations of clinical systems to detect environmental contaminants in products is important as the demand for cell therapy expands in the clinical setting.